Merge branch 'master' into dependabot/pip/setuptools-65.5.1

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.6.9
+current_version = 2.7.0
 commit = True
 tag = True
 tag_name = {new_version}

.github/workflows/build_and_publish.yml

@@ -9,13 +9,13 @@ on:
 jobs:
  build-n-publish:
   name: Build and publish Python distribution to PyPI
-  runs-on: ubuntu-18.04
+  runs-on: ubuntu-latest
   steps:
    - name: Check out git repository
-     uses: actions/checkout@v2
+     uses: actions/checkout@v3
 
    - name: Set up Python 3.9
-     uses: actions/setup-python@v2
+     uses: actions/setup-python@v4
      with:
       python-version: 3.9
 

.github/workflows/tests.yml

@@ -13,11 +13,11 @@ jobs:
 
     steps:
     # Check out Scout code
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
 
     # Set up python
     - name: Set up Python ${{ matrix.python-version}}
-      uses: actions/setup-python@v1
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version}}
 
@@ -30,7 +30,7 @@ jobs:
     - name: Production Dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install -e .
+        pip install -e . 
 
     - name: Dev Dependencies
       run: |

docs/user-guide/loading.md

@@ -35,7 +35,7 @@ Options:
   -s, --skip-case-id              Do not store case information on variants
                                   [default: False]
   --ensure-index                  Make sure that the indexes are in place
-  --gq-treshold INTEGER           Treshold to consider variant  [default: 20]
+  --gq-threshold INTEGER           Threshold to consider variant  [default: 20]
   -m, --max-window INTEGER        Specify the maximum window size for svs
                                   [default: 2000]
   --check-profile PATH            Apply sample profiling for the samples,

loqusdb/build_models/variant.py

@@ -139,19 +139,19 @@ def get_coords(variant):
     return coordinates
 
 
-def build_variant(variant, case_obj, case_id=None, gq_treshold=None, genome_build=None):
+def build_variant(variant, case_obj, case_id=None, gq_threshold=None, gq_qual=False, genome_build=None):
     """Return a Variant object
 
     Take a cyvcf2 formated variant line and return a models.Variant.
 
     If criterias are not fullfilled, eg. variant have no gt call or quality
-    is below gq treshold then return None.
+    is below gq threshold then return None.
 
     Args:
         variant(cyvcf2.Variant)
         case_obj(Case): We need the case object to check individuals sex
         case_id(str): The case id
-        gq_treshold(int): Genotype Quality treshold
+        gq_threshold(int): Genotype Quality threshold
 
     Return:
         formated_variant(models.Variant): A variant dictionary
@@ -188,8 +188,14 @@ def build_variant(variant, case_obj, case_id=None, gq_treshold=None, genome_buil
             ind_id = ind_obj["ind_id"]
             # Get the index position for the individual in the VCF
             ind_pos = ind_obj["ind_index"]
-            gq = int(variant.gt_quals[ind_pos])
-            if gq_treshold and gq < gq_treshold:
+
+            if gq_qual:
+                gq = int(variant.QUAL)
+
+            if not gq_qual:
+                gq = int(variant.gt_quals[ind_pos])
+
+            if gq_threshold and gq < gq_threshold:
                 continue
 
             genotype = GENOTYPE_MAP[variant.gt_types[ind_pos]]

loqusdb/commands/load.py

@@ -54,7 +54,8 @@ def validate_profile_threshold(ctx, param, value):
     help="Do not store case information on variants",
 )
 @click.option("--ensure-index", is_flag=True, help="Make sure that the indexes are in place")
-@click.option("--gq-treshold", default=20, show_default=True, help="Treshold to consider variant")
+@click.option("--gq-threshold", default=20, show_default=True, help="Threshold to consider variant")
+@click.option("--qual-gq", is_flag=True, default=False, show_default=True, help="Use QUAL tag instead of GQ value for quality filter")
 @click.option(
     "--max-window",
     "-m",
@@ -89,13 +90,14 @@ def load(
     family_file,
     family_type,
     skip_case_id,
-    gq_treshold,
+    gq_threshold,
     case_id,
     ensure_index,
     max_window,
     check_profile,
     hard_threshold,
     soft_threshold,
+    qual_gq
 ):
     """Load the variants of a case
 
@@ -136,7 +138,8 @@ def load(
             family_type=family_type,
             skip_case_id=skip_case_id,
             case_id=case_id,
-            gq_treshold=gq_treshold,
+            gq_threshold=gq_threshold,
+            qual_gq=qual_gq,
             max_window=max_window,
             profile_file=variant_profile_path,
             hard_threshold=hard_threshold,

loqusdb/commands/update.py

@@ -47,7 +47,7 @@
     help="Do not store case information on variants",
 )
 @click.option("--ensure-index", is_flag=True, help="Make sure that the indexes are in place")
-@click.option("--gq-treshold", default=20, show_default=True, help="Treshold to consider variant")
+@click.option("--gq-threshold", default=20, show_default=True, help="Threshold to consider variant")
 @click.option(
     "--max-window",
     "-m",
@@ -63,7 +63,7 @@ def update(
     family_file,
     family_type,
     skip_case_id,
-    gq_treshold,
+    gq_threshold,
     case_id,
     ensure_index,
     max_window,
@@ -102,7 +102,7 @@ def update(
             family_type=family_type,
             skip_case_id=skip_case_id,
             case_id=case_id,
-            gq_treshold=gq_treshold,
+            gq_threshold=gq_threshold,
             max_window=max_window,
         )
     except (SyntaxError, CaseError, IOError, VcfError) as error:

loqusdb/utils/load.py

@@ -31,7 +31,8 @@ def load_database(
     family_file=None,
     family_type="ped",
     skip_case_id=False,
-    gq_treshold=None,
+    gq_threshold=None,
+    qual_gq=False,
     case_id=None,
     max_window=3000,
     profile_file=None,
@@ -48,7 +49,8 @@ def load_database(
           family_file(str): Path to family file
           family_type(str): Format of family file
           skip_case_id(bool): If no case information should be added to variants
-          gq_treshold(int): If only quality variants should be considered
+          gq_threshold(int): If only quality variants should be considered
+          qual_gq(bool): Use QUAL field instead of GQ format tag to gate quality
           case_id(str): If different case id than the one in family file should be used
           max_window(int): Specify the max size for sv windows
           check_profile(bool): Does profile check if True
@@ -87,13 +89,13 @@ def load_database(
             adapter, profiles, hard_threshold=hard_threshold, soft_threshold=soft_threshold
         )
 
-    # If a gq treshold is used the variants needs to have GQ
+    # If a gq threshold is used the variants needs to have GQ
     for _vcf_file in vcf_files:
         # Get a cyvcf2.VCF object
         vcf = get_vcf(_vcf_file)
 
-        if gq_treshold and not vcf.contains("GQ"):
-            LOG.warning("Set gq-treshold to 0 or add info to vcf {0}".format(_vcf_file))
+        if gq_threshold and not vcf.contains("GQ") and not qual_gq:
+            LOG.warning("Set gq-threshold to 0 or add info to vcf {0}".format(_vcf_file))
             raise SyntaxError("GQ is not defined in vcf header")
 
     # Get a ped_parser.Family object from family file
@@ -143,7 +145,8 @@ def load_database(
                 vcf_obj=vcf_obj,
                 case_obj=case_obj,
                 skip_case_id=skip_case_id,
-                gq_treshold=gq_treshold,
+                gq_threshold=gq_threshold,
+                qual_gq=qual_gq,
                 max_window=max_window,
                 variant_type=variant_type,
                 genome_build=genome_build,
@@ -189,7 +192,8 @@ def load_variants(
     vcf_obj,
     case_obj,
     skip_case_id=False,
-    gq_treshold=None,
+    gq_threshold=None,
+    qual_gq=False,
     max_window=3000,
     variant_type="snv",
     genome_build=None,
@@ -202,7 +206,7 @@ def load_variants(
         nr_variants(int)
         skip_case_id (bool): whether to include the case id on variant level
                              or not
-        gq_treshold(int)
+        gq_threshold(int)
         max_window(int): Specify the max size for sv windows
         variant_type(str): 'sv' or 'snv'
 
@@ -222,7 +226,7 @@ def load_variants(
     with click.progressbar(vcf_obj, label="Inserting variants", length=nr_variants) as bar:
 
         variants = (
-            build_variant(variant, case_obj, case_id, gq_treshold, genome_build=genome_build)
+            build_variant(variant, case_obj, case_id, gq_threshold, qual_gq, genome_build=genome_build)
             for variant in bar
         )
 

loqusdb/utils/update.py

@@ -28,7 +28,7 @@ def update_database(
     family_file=None,
     family_type="ped",
     skip_case_id=False,
-    gq_treshold=None,
+    gq_threshold=None,
     case_id=None,
     max_window=3000,
 ):
@@ -41,7 +41,7 @@ def update_database(
           family_file(str): Path to family file
           family_type(str): Format of family file
           skip_case_id(bool): If no case information should be added to variants
-          gq_treshold(int): If only quality variants should be considered
+          gq_threshold(int): If only quality variants should be considered
           case_id(str): If different case id than the one in family file should be used
           max_window(int): Specify the max size for sv windows
 
@@ -67,14 +67,14 @@ def update_database(
         vcf_files.append(sv_file)
         sv_individuals = vcf_info["individuals"]
 
-    # If a gq treshold is used the variants needs to have GQ
+    # If a gq threshold is used the variants needs to have GQ
     for _vcf_file in vcf_files:
         # Get a cyvcf2.VCF object
         vcf = get_vcf(_vcf_file)
 
-        if gq_treshold:
+        if gq_threshold:
             if not vcf.contains("GQ"):
-                LOG.warning("Set gq-treshold to 0 or add info to vcf {0}".format(_vcf_file))
+                LOG.warning("Set gq-threshold to 0 or add info to vcf {0}".format(_vcf_file))
                 raise SyntaxError("GQ is not defined in vcf header")
 
     # Get a ped_parser.Family object from family file
@@ -127,7 +127,7 @@ def update_database(
                 vcf_obj=vcf_obj,
                 case_obj=case_obj,
                 skip_case_id=skip_case_id,
-                gq_treshold=gq_treshold,
+                gq_threshold=gq_threshold,
                 max_window=max_window,
                 variant_type=variant_type,
             )

requirements.txt

@@ -7,7 +7,7 @@ numpy==1.21.4
 coloredlogs==14.0
 pyyaml==5.4.0
 vcftoolbox==1.5
-pip==21.3.1
+pip==23.1.2
 setuptools==65.5.1
 mongo_adapter>=0.3.3
 ped_parser

setup.py

@@ -10,8 +10,6 @@
 import io
 import os
 
-from pip._internal.network.session import PipSession
-from pip._internal.req import parse_requirements
 from setuptools import find_packages, setup
 
 # Package meta-data.
@@ -21,13 +19,10 @@
 EMAIL = "mans.magnusson@scilifelab.com"
 AUTHOR = "Måns Magnusson"
 REQUIRES_PYTHON = ">=3.7.0"
-VERSION = "2.6.9"
-
-requirements = [
-    requirement.requirement
-    for requirement in parse_requirements(filename="./requirements.txt", session=PipSession())
-]
+VERSION = "2.7.0"
 
+with open('requirements.txt') as f:
+    install_requires = f.read().strip().split('\n')
 
 # The rest you shouldn't have to touch too much :)
 # ------------------------------------------------
@@ -68,7 +63,7 @@
     entry_points={
         "console_scripts": ["loqusdb = loqusdb.__main__:base_command"],
     },
-    install_requires=requirements,
+    install_requires=install_requires,
     include_package_data=True,
     license="MIT",
     keywords=["vcf", "variants"],

tests/conftest.py

@@ -319,7 +319,7 @@ def variant_obj(request, het_variant, ind_positions, individuals):
         individuals=individuals,
         ind_positions=ind_positions,
         case_id="test",
-        gq_treshold=None,
+        gq_threshold=None,
     )
 
 

tests/vcf_tools/test_format_variant.py

@@ -25,9 +25,9 @@ def test_format_variant_no_gq(variant_no_gq, case_obj):
     ## GIVEN a variant without GQ
     variant = variant_no_gq
     case_id = case_obj["case_id"]
-    ## WHEN parsing the variant using a GQ treshold
+    ## WHEN parsing the variant using a GQ threshold
     formated_variant = build_variant(
-        variant=variant, case_obj=case_obj, case_id=case_id, gq_treshold=20
+        variant=variant, case_obj=case_obj, case_id=case_id, gq_threshold=20
     )
     ## THEN assert that None is returned since requirements are not fulfilled
     assert formated_variant is None
@@ -38,9 +38,9 @@ def test_format_variant_chr_prefix(variant_chr, case_obj):
     variant = variant_chr
     assert variant.CHROM.startswith("chr")
     case_id = case_obj["case_id"]
-    ## WHEN parsing the variant using a GQ treshold
+    ## WHEN parsing the variant using a GQ threshold
     formated_variant = build_variant(
-        variant=variant, case_obj=case_obj, case_id=case_id, gq_treshold=20
+        variant=variant, case_obj=case_obj, case_id=case_id, gq_threshold=20
     )
     ## THEN assert that the 'chr' part has been stripped away
     assert formated_variant["chrom"] == variant.CHROM[3:]